Summary of my professional life
David Jimenez-Morales
PhD, MSc, BSc
Summary of my professional life
2006 - 2013
PhD Bioinformatics
Department of Bioengineering. University of Illinois at Chicago. Chicago, Illinois (USA)
2003 - 2004
MSc Computational Biology
Universidad Complutense de Madrid. Madrid (Spain)
1999
Teaching Certificate (Postgraduate Certificate in Education)
Instituto de Ciencias de la Educación. Universidad Complutense de Madrid. Madrid (Spain)
1998 - 2000
Microbiology PhD Program and Research Certificate
Department of Microbiology I, Universidad Complusense de Madrid.
1993 - 1998
BSc Biology
Facultad de Ciencias. Universidad de Granada. Granada (Spain)
2018 -
Senior Computational Biologist (Staff Scientist)
The Ashley lab. Department of Medicine, Division of Cardiovascular Medicine. Stanford University
2015 - 2018
Researcher (Staff Scientist)
The Krogan lab. Department of Cellular and Molecular Pharmacology (CMP). University of California San Francisco (UCSF)
2016 - 2018
Visiting Scientist
Gladstone Institutes. San Francisco, CA
2013 - 2018
Bioengineering Department Affiliate
Department of Bioengineering. University of Illinois-Chicago. Chicago
2014 - 2015
Research Associate (Software Developer and Bioinformatics Specialist)
dictyBase.org. Center for Genetic Medicine. Northwestern University. Chicago
2013 - 2015
Visiting Research Associate
Shannon Hackett's lab. Bird Division. The Field Museum of Natural History. Chicago
2013 - 2014
Visiting Instructor
Prof Bob Eisenberg’s Lab. Department of Molecular. Biophysics & Physiology. Rush University Medical Center. Chicago.
2006 - 2013
PhD Graduate Student
Jie Liang’s Molecular and Systems Computational lab. Department of Bioengineering. University of Illinois-Chicago. Chicago
2003 - 2005
Research Assistant
Proteomics Unit & Department of Microbiology II. Universidad Complutense de Madrid – Parque Científico de Madrid. Madrid
1998 - 2000
Research Assistant
Department of Microbiology I. Faculty of Medicine. Universidad Complutense de Madrid. Madrid.
2018 - Krystal A Fontaine, Kristoffer E Leon, Mir Mubashir Khalid, David Jimenez-Morales, Julia Kaye, Priya Shah, Steven Finkbeiner, Nevan Krogan, Melanie Ott
The cellular NMD pathway restricts Zika virus infection and is targeted by the viral capsid protein
Pre-printed at bioRxiv. mBio. In press
2018 - Nan Zhao, Vittorio Sebastiano, Natasha Moshkina, Nacho Mena, Judd Hultquist, David Jimenez-Morales, Yixuan Ma, Alexander Rialdi, Randy Albrecht, Romain Fenouil, Maria Teresa Sanchez-Aparicio, Juan Ayllon, Sweta Ravisankar, Bahareh Haddad, Jessica Sook Yuin Ho, Diana Low, Jian Jin, Yurchenko Vyacheslav, Rabinder Prinjha, Alexander Tarakhovsky, Massimo Squatrito, Dalila Pinto, Allette Kimaada, Minji Byun, Melissa Smith, Robert Sebra, Ernesto Guccione, Terrence Tumpey, Nevan Krogan, Harm van Bakel, Benjamin Greenbaum, Adolfo Garcia-Sastre, and Ivan Marazzi
Influenza virus infection causes global RNAPII termination defects
Nature Structural & Molecular Biology. 2018 Sep;25(9):885-893. doi: 10.1038/s41594-018-0124-7. Epub 2018 Sep 3.
2018 - Esther Paulo, Dongmei Wu, Yangmeng Wang, Yun Zhang, Yixuan Wu, Danielle L. Swaney, Margaret Soucheray, David Jimenez-Morales, Ajay Chawla, Nevan J. Krogan & Biao Wang
Sympathetic inputs regulate adaptive thermogenesis in brown adipose tissue through cAMP-Salt inducible kinase axis.
Sci Rep. 2018 Jul 20; 8(1):11001
2018 - Kristin L. Patrick, Jason A. Wojcechowskyj, Tao Jing, Morgan Riba, Sara Talmage, Pengbiao Xu, Samantha L. Bell, Ana L. Cabello, Jiewei Xu, Michael Shales, David Jimenez-Morales, Thomas A. Ficht, Paul de Figueiredo, James E. Samuel1, Pingwei Li, Nevan J. Krogan, Robert O. Watson
Quantitative yeast genetic interaction profiling of bacterial effector proteins uncovers a role for the human retromer in Salmonella infection
2018 - Ruchi Masand, Esther Paulo, Dongmei Wu , Yangmeng Wang, Danielle L. Swaney, David Jimenez-Morales, Nevan J. Krogan, and Biao Wang
Proteome Imbalance of Mitochondrial Electron Transport Chain in Brown Adipocytes Leads to Metabolic Benefits.
Cell Metab. 2018 Mar 06; 27(3):616-629.e4
2017 - Rialdi A, Hultquist J, Jimenez-Morales D, Peralta Z, Campisi L, Fenouil R, Moshkina N, Wang Zhen Z, Laffleur B, Michael R, Haas K, Pefanis E, Albrecht A. R, Jen J, Basu U, Garcia-Sastre A, van Bakel H, Krogan N, Marazzi I
The RNA Exosome Syncs IAV-RNAPII Transcription to Promote Viral Ribogenesis and Infectivity.
Cell 2017 May 4;169(4):679-692.e14.
2015 - Basu S, Fey P, Jimenez-Morales D, Dodson RJ, Chisholm RL
dictyBase 2015: Expanding data and annotations in a new software environment.
Genesis 2015 Jun 19.
2014 - Jimenez-Morales D, Adamian L, Shi D, and Liang J.
Lysine Carboxylation: Unveiling a spontaneous posttranslational modification.
Acta Crystallogr D Biol Crystallogr. 2014 Jan;70(Pt 1):48-57
2012 - Jimenez-Morales D, Liang J, and Eisenberg B.
Ionizable Side Chains at Catalytic Active Sites of Enzymes.
Eur Biophys J. Vol 41, Issue 5 (2012), P 449-460.
2012 - Naveed H, Jimenez-Morales D, Tian J, Pasupuleti V, Kenney L, Liang L (2012).
Engineered oligomerization state of OmpF protein through computational design decouples oligomer dissociation from unfolding.
J Mol Biol. 2012 May 25;419(1-2):89-101.
2011 - Liang J, Naveed H, Jimenez-Morales D, Adamian L, Lin M.
Computational studies of membrane proteins: Models and predictions for biological understanding.
Biochim Biophys Acta. 2011 Oct 12.
2011 - Jimenez-Morales D and Liang J.
Pattern of Amino Acid Substitutions in Transmembrane Domains of β-Barrel Membrane Proteins for Detecting Remote Homologs in Bacteria and Mitochondria.
PLoS ONE. 2011;6(11):e26400. Epub 2011 Nov 1.
2008 - Jimenez-Morales D, Adamian L, and Liang J.
Detecting Remote Homologues Using Scoring Matrices Calculated from the Estimation of Amino Acid Substitution Rates of Beta-Barrel Membrane Proteins.
Conf Proc IEEE Eng Med Biol Soc. 2008, 30:1347-1350.
2008 - Jimenez-Morales D.
Substitution Rates of Amino Acid residues in Transmembrane Regions of Beta-Barrel Membrane Proteins.
BioE Student Journal. N1, 2008. Front Cover.
2001 - Coauthor.
Propiedades adicionales no antibióticas de los macrólidos.
Scientific Communication Management Editors.
2001 - Coauthor.
Guía Setas Autóctonas.
Editorial Doyma. Madrid.
2000 - Jimenez-Morales D.
Problematic in the use of antiobiotics in animal farms.
Nº41. Ganaderos Magazine. sp
2000 - Jimenez-Morales D.
Bovine spongiform encephalopathy.
Nº37. Ganaderos Magazine.
2017 - David Jimenez-Morales, Judd Hultquist, John Von Dollen, Jeff Johnson, Hannes Braberg, and Nevan J Krogan
Influenza virus networks of pathogenesis inferred from the integration of multiple large-scale datasets.
Annual Programmatic Meeting. NIAID-NIH, Systems Biology for Infectious Diseases (SBID) Research. May 7-10, 2017 Chicago, IL.
2017 - Kelsey Haas, Michael McGregor, David Jimenez-Morales, Judd Hultquist and Nevan Krogan
Destroying the “Non-self”: Defining Influenza A Viral Endonuclease Mechanisms for Host Shutoff.
Annual Programmatic Meeting. NIAID-NIH, Systems Biology for Infectious Diseases (SBID) Research. May 7-10, 2017 Chicago, IL.
2017 - Judd F. Hultquist, David Jimenez-Morales, Michael M. McGregor, Kelsey Haas, Jeffrey Johnson, William Newton, Giorgi Metreveli, Matthew Urbanowski, Megan Shaw, Ivan Marazzi, Randy A. Albrecht, Adolfo Garcia-Sastre, and Nevan J. Krogan
Proteomic Profiling of Influenza A Virus Infection Reveals Strain-specific Rewiring of Host Cell Networks.
Annual Programmatic Meeting. NIAID-NIH, Systems Biology for Infectious Diseases (SBID) Research. May 7-10, 2017 Chicago, IL.
2017 - Celina Cahalane, David Jimenez-Morales, John VonDollen, Hannah Baumann, Matthew Urbanowksi, Megan Shaw, Giorgi Metreveli, Nevan Krogan, Adolfo Garcia-Sastre, Oswald Quehenberger, Edward Dennis, and Leah Shriver
Metabolic Profiling of Influenza Infection.
Annual Programmatic Meeting. NIAID-NIH, Systems Biology for Infectious Diseases (SBID) Research. May 7-10, 2017 Chicago, IL.
2016 - Jimenez-Morales D, Von Dollen J, Braberg H, Verschueren E, and Krogan NJ.
Predictive models for the identification of networks involved in host responses to influenza virus infection.
2nd Annual Host- Pathogen Interactions: Circuits to Systems Symposium. Jan 4, 2016. San Diego, CA.
2011 - Jimenez-Morales D, Liang J, and Eisenberg B.
Active Sites of Enzymes are Crowded with Charge.
Biophysical Journal. 100(3): p. 218a. Abstract 1191-Pos and Poster Board B101.
2011 - Jimenez-Morales D, Liang J, and Eisenberg B.
Active Sites of Enzymes are Crowded with Charge.
6th Annual Midwest Conference on Protein Folding, Assembly, and Molecular Motions. University of Notre Dame.
2010 - Jimenez-Morales D, Li R, Wang Z, Li Y, Liu L, Liang J.
Evolutionary Speed of Enzymes Functional Surfaces and their Relationship with Metabolic Fluxes in Networks of Central Carbon Metabolism of Bacteria.
Biophysical Journal 98(3) pp. 741a
2008 - Jimenez-Morales D, Adamian L, Liang J.
Substitution Rates Of Amino Acid Residues In Transmembrane - Extracellular And Periplasmic- Regions Of Beta-Barrel Membrane Proteins.
Biophysical Journal 94(2) pp. 1959
2002 - Jimenez-Morales D.
Tools for the Apored Virtual.
V-Aporeunión. Tordesillas (Valladolid). Oral presentation: I introduced the improvements in the new Apoweb.
1999 - Jimenez-Morales D, Heredia S, Calvo A, Gomez-Luz ML, Prieto J.
Sensibilidad a antimicrobianos de Enterococcus faecalis de procedencia animal.
Spanish Chemotherapy Society Congress. May 1999
As Instructor. Department of Bioengineering. University of Illinois at Chicago.
Fall 2010 - BIOE480: Introduction to Bioinformatics.
Fall 2012 - BIOE481: Bioinformatics Laboratory.
As Teaching Assistant. Department of Bioengineering. University of Illinois at Chicago.
Spring 2013 - BIOE250, Clinical Problems in Bioengineering .
Fall 2012 - BIOE481: Bioinformatics Laboratory.
Fall 2010, 2012 - BIOE480, Introduction to Bioinformatics.
Spring 2007 - BIOE455, Intro to Cell and Tissue Engineering .
Fall 2006 - BIOE240, Modeling Physiological Data & Systems
Operating Systems: Unix/Linux and Mac OS X. Virtual Computing: Docker, Vagrant.
Bioinformatics Packages. Sequence analysis software (Blast, MEME-MAST, ClustalW, T-Coffee, HMMER, HHsearch,...); Molecular structures visualization software (PyMOL, VMD, Rasmol, Dino, SPDBV); Molecular dynamics (NAMD); Molecular interactions (Mint, Osprey); Genomics: Maker, FastQC, ALLPATHS-LG, Circos, GeneMark, QIIME, Galaxy; etc
Programming languages: R (also Shiny), Perl, Unix shell scripts, HTML, CSS (Bootstrap), Javascript (AngularJS, Node.js), Ruby on Rails, PHP, Matlab, C/C++, Java.
Databases: Relational: PostgreSQL & MySQL. SQL language. Generic Model Organism Database Chado schema of relational databases. NoSQL databases: Neo4j. Search engine: elasticsearch
GMOD tools: JBrowse, WebApollo, InterMine.
Others: Source code management (git/github); Design (Photoshop); Statistician (R, SAS, SPSS).
I have developed the following tools:
bioNeNa (the FluOMICS bioNetwork Navigator): a systems biology tool to explore large-scale datasets.
R package: artMS: Analytical R Tools for Mass Spectrometry. Check the Github repo and the bioConductor page
.MIDTOD: Metabolite Identification Through Orthogonal Datasets (under development).
PreLysCar (Predictor of Lysine Carboxylation), also available as a tool at the suite of programs CCP4.
bbTM-ST (beta-barrel TransMembrane Search Tool) .
2017 - Krogan Lab. UCSF. San Francisco, CA (USA)
2016 - FluOMICS. UCSF. San Francisco, CA (USA)
2016 - New Dictybase. Dictybase. Northwestern University. Chicago (IL, USA)
2015 - dictyMeeting 2015. Dictybase. Northwestern University. Chicago (IL, USA)
2003 - Proteomic Unit . Facultad de Farmacia. UCM-PCM (Madrid, Spain)
2002, 2005 - Spanish Network of Apoptosis (APORED) Department of Cell and Developmental Biology. Centro de Investigaciones Biológicas (CIB-CSIC)
2002 - 2005 - Spanish Network of Apoptosis (APORED) . Department of Cell and Developmental Biology. CIB-CSIC. Administrator of workspace BSCW (Basic Support for Cooperative Work) of the APORED. List co-administrator of APORED email distribution list, and list administrator of Apobecarios email distribution list. Website updates
U19AI135972: “FluOMICS, The Next Generation”.
2018 – 2022. Co-PI Modeling Core. Co-PI Data Management and Bioinformatics Core (DMBC). NIH/NIAID
Pilot Project (U19AI106754): “Development of a web-based computational tool for integrating and navigating systems biology data and models”.
2017 – 2018. Principal Investigator. NIH/NIAID
Beca Talentia Excellence Grant
2008 - 2010. Regional Ministry for Innovation, Science and Enterprise. Junta de Andalucía. Spain.
